A relational database to identify differentially expressed genes in the endometrium and endometriosis lesions

Endometriosis is a common inflammatory estrogen-dependent gynecological disorder, associated with pelvic pain and reduced fertility in women. Several aspects of this disorder and its cellular and molecular etiology remain unresolved. We have analyzed the global gene expression patterns in the endometrium, peritoneum and in endometriosis lesions of endometriosis patients and in the endometrium and peritoneum of healthy women. In this report, we present the EndometDB, an interactive web-based user interface for browsing the gene expression database of collected samples without the need for computational skills. The current database incorporates the expression data from 115 patients and 53 controls, with over 24000 genes and clinical features, such as their age, disease stages, hormonal medication, menstrual cycle phase, and the different endometriosis lesion types. Using the web-tool, the end-user can easily generate various plot outputs, including boxplots, heatmaps and scatterplots, and the generated plot outputs can be downloaded in pdf-format. Availability and implementation: The web-based user interface is implemented using HTML5, JavaScript, CSS, Plotly and R. It is freely available from URL: https://endometdb.utu.fi/gene_analysis.<br>Endomet Database dump and schema.<br><br>Number of samples used in quantitative real-time PCR.<br><br>Pie chart showing the percentage of the different types of samples analyzed for global gene expression by microarrays.<br>Multidimensional scaling of WNT pathway genes of the endometrium vs endometriosis samples using Canberra distance metric and colored by tissues.<b> </b>The analysis separates endometrial specimens from the different lesions<b>.</b><b><br></b>Result of scree test for PCA analysis of WNT pathway genes. The scree plot explains how much the principal components account for the total variance in the expression data.<b><br></b>子宫内膜异位症（Endometriosis）是一种常见的炎症性雌激素依赖性妇科疾病，与女性盆腔疼痛及生育能力下降密切相关。目前该疾病的诸多方面及其细胞与分子病因仍未得到明确阐释。 本研究团队对子宫内膜异位症患者的子宫内膜、腹膜组织及异位病灶，以及健康女性的子宫内膜与腹膜组织开展了全基因表达谱分析。在本研究报告中，我们推出了EndometDB——一款基于网页的交互式用户界面，可供不具备计算技能的使用者便捷浏览本研究收集的基因表达数据库。 当前数据库整合了115例患者与53例健康对照的表达数据，涵盖超过24000个基因以及患者的多项临床特征，包括年龄、疾病分期、激素用药情况、月经周期阶段以及不同类型的子宫内膜异位症病灶。 通过该网页工具，终端用户可轻松生成多种可视化绘图结果，包括箱线图、热图与散点图，且生成的绘图文件可导出为PDF格式。 可用性与实现说明：该网页用户界面基于HTML5、JavaScript、CSS、Plotly及R语言开发，可通过以下网址免费访问：https://endometdb.utu.fi/gene_analysis。 子宫内膜数据库导出文件与数据库架构。 实时定量PCR（quantitative real-time PCR）所用样本数量统计。 展示通过微阵列（microarrays）开展全基因表达谱分析的各类样本占比的饼图。 基于堪培拉距离（Canberra distance）度量的子宫内膜样本与子宫内膜异位症样本的WNT通路（WNT pathway）基因多维尺度分析结果，按组织类型着色。该分析可将子宫内膜标本与不同类型的异位病灶区分开来。 针对WNT通路基因的主成分分析（Principal Component Analysis, PCA）碎石检验结果。碎石图用于展示各主成分对表达数据总方差的解释占比。